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Crystal structure of duplex DNA3 in complex with Hg(II) and Sr(II)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 10% v/v MPD, 40 mM Sodium cacodylate, 12 mM Spermine tetra-HCl, 40 mM LiCl, 80 mM SrCl2
Crystal Properties Matthews coefficient Solvent content 2.1 41.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.318 α = 90 b = 40.318 β = 90 c = 24.98 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2013-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97928 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.05 30 96.4 16.8 6.9 9769
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.05 18.8 8921 444 93.27 0.14374 0.14038 0.1459 0.15577 0.1537 RANDOM 21.342
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.26 0.26 -0.52
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 59.824 r_sphericity_bonded 9.641 r_angle_other_deg 1.379 r_rigid_bond_restr 1.184 r_angle_refined_deg 0.839 r_chiral_restr 0.052 r_gen_planes_refined 0.009 r_bond_refined_d 0.004 r_bond_other_d 0.004 r_gen_planes_other 0.001
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 59.824 r_sphericity_bonded 9.641 r_angle_other_deg 1.379 r_rigid_bond_restr 1.184 r_angle_refined_deg 0.839 r_chiral_restr 0.052 r_gen_planes_refined 0.009 r_bond_refined_d 0.004 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 160 Solvent Atoms 44 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling SHELXDE phasing